getPathwayForGeneId: Get pathways associated to a gene.

In AtlasRDF: Gene Expression Atlas query and gene set enrichment package.

Description

Get signalling pathways from Reactome that are associated to a gene, via associated protein(s) which are in turn connected to said signalling patwhay(s) in Reactome.

Usage

getPathwayForGeneId(geneid, endpoint = "http://www.ebi.ac.uk/rdf/services/atlas/sparql")

Arguments

geneid	The ENSEMBL ID for a gene.
endpoint	SPARQL endpoint to query data from. Default value is the live Atlas SPARQL endpoint but this can be overidden.

Value

List of pathway URIs.

Author(s)

James Malone, Simon Jupp

Examples

###get pathways for the gene SNHG5
#getPathwayForGeneId("http://identifiers.org/ensembl/ENSG00000203875")

AtlasRDF documentation built on Nov. 17, 2017, 9:33 a.m.